Effect of van der Waals interactions on H<Subscript>2</Subscript> dissociation on clean and defected Ru(0001) surface

Ab initio computational methods are used to study the relevance of van der Waals interactions in the case of a hydrogen molecule adsorption on the Ru(0001) surface. In addition to the clean surface, the effects of ruthenium adatom and vacancy on the process are studied. The adsorption characteristics are analyzed in terms of two dimensional cuts of the potential energy surface (PES). Based on the earlier studies for such systems, we mostly concentrate on the trajectories where the hydrogen molecule approaches the surface in parallel orientation. The results indicate that for a clean Ru(0001) the calculations applying the non-local van der Waals potentials yield higher barriers for the dissociation of the H₂ molecule. Of the high symmetry sites on Ru(0001), the top site is found to be the most reactive one. The vacancy and ruthenium adatom sites exhibit high dissociation barriers compared with the clean surface.     

Adsorption configurations of carbon monoxide on gold monolayer supported by graphene or monolayer hexagonal boron nitride: a first-principles study

Using density functional theory with a semiempirical van der Waals approach proposed by Grimme, the adsorption behavior of carbon monoxide on a gold monolayer supported by graphene or monolayer hexagonal boron nitride has been investigated. Based on the changes in the Dirac cone of graphene and a Bader charge analysis, we observe that the Au(111) monolayer gains a small charge from graphene and monolayer h-BN. The adsorbed CO molecule adopts similar adsorption configurations on Au(111)/graphene and Au(111)/h-BN with Au-C distance 2.17?2.50 Å and Au-C-O angle of 123.9°–139.6°. Moreover, we found that for low CO coverages, bonding to the gold surface is surprisingly energy-favorable. Yet the CO adsorption binding energy diminishes at high coverage due to the repulsive van der Waals interactions between CO molecules.     

不同覆盖度下丙硫醇在Au(111)面吸附的理论研究

采用基于密度泛函理论的第一性原理方法研究了丙烷硫醇 (C₃H₇SH)在Au(111)面五种覆盖度(1/16, 2/16, 3/16, 4/16, 1/3) 下的未解离和解离吸附的结构、能量和吸附性质. 发现丙烷硫醇的倾斜角和吸附能均受覆盖度影响, 计算结果显示丙烷硫醇的倾斜角随着覆盖度的增大减小了6°–10°, 吸附能随覆盖度的增大减小了0.21 eV. 特别针对饱和覆盖度, 研究了三种可能的表面结构: (2√3×2√3 ight)R30°, 2√3×3和(3×3). 发现S–H键未解离时三种表面结构的吸附构型和吸附能基本一致; S–H键解离后, (2√3×2√3 ight)R30°和2√3×3结构的吸附能比以(3×3)结构的吸附能约高0.05–0.07 eV, 说明C₃H₇S在Au(111)面吸附时, 倾向于形成(2√3×2√3 ight)R30°和2√3×3结构. 此外, 采用DFT-D2方法对饱和覆盖度下C₃H₇SH分子在Au(111)面的吸附进行了范德华修正, 结果显示分子间相互作用使吸附物和Au表面的距离减小, 该相互作用对吸附能的修正值为0.53 eV, 修正后结果与实验结果接近. 关键词： 第一性原理 覆盖度 表面结构 范德华力     

Importance of van der Waals interaction for organic molecule-metal junctions: adsorption of thiophene on Cu(110) as a prototype

We report ab initio calculations for the interface energetics of a weakly adsorbed organic molecule on a metal surface, which serves as a model interface relevant for organic electronics. The studied thiophene ring is found to be physisorbed on the Cu(110) surface with an adsorption energy of -0.50 eV. Nonlocal correlations, i.e., van der Waals interactions, are solely responsible for the binding in this weakly interacting system, and the choice of the proper exchange-correlation function is crucially important. The adsorption of thiophene lowers the metal work function due to the formation of surface dipoles while no sizable charge transfer is found.     

Methane molecule over the defected and rippled graphene sheet

Adsorption of a methane molecule (CH₄) onto a defected and rippled graphene sheet is studied using ab initio and molecular mechanics calculations. The optimal adsorption position and orientation of this molecule on the graphene surface (motivated by the recent realization of graphene sensors to detect individual gas molecules) is determined and the adsorption energies are calculated. In light of the density of states, we used the SIESTA code. It is found that (i) classical force field yields adsorption energy comparable with experimental result and ab initio calculation; (ii) the periodic nature of the van der Waals potential energy stored between methane and perfect sheet is altered due to the insertion vacancies and sinusoidal ripples; (iii) the van der Waals potential energy is found to be sensitive to the presence of the vacancies and the ripples so that the added molecule avoids to be around vacant cites and on top of the peaks.     

分子动力学模拟研究方解石表面润湿性反转机理

利用分子动力学模拟技术从分子尺度探究方解石表面润湿性反转机理.首先,研究方解石表面润湿性反转过程;而后,从原油分子-方解石表面与原油分子-原油分子/水分子相互作用两个方面系统揭示方解石表面润湿性反转机理.结果:(1)水分子能够驱离方解石表面弱吸附的非极性分子造成润湿性的改变,但不能驱离强吸附的极性分子使润湿性反转难以实现;(2)原油分子极性越强与方解石表面相互作用越强,极性分子与方解石表面之间主要为静电力,非极性分子与方解石表面之间主要为范德华力;(3)原油分子极性越相近分子之间的相互作用越强,分子极性相差越大分子之间的相互作用越弱.非极性分子之间主要是范德华力,极性分子之间主要是静电力;(4)原油分子在方解石表面和水分子的共同作用下形成乙酸-吡啶-水-甲苯-己烷的稳定吸附序列.本研究为靶向提高采收率技术的设计与应用提供理论基础.     

Application of van der Waals density functional to an extended system: adsorption of benzene and naphthalene on graphite

It is shown that it is now possible to include van der Waals (vdW) interactions via a nonempirical implementation of density functional (DF) theory to describe the correlation energy in electronic structure calculations on infinite systems of no particular symmetry. The vdW-DF theory [Phys. Rev. Lett. 92, 246401 (2004)] is applied to the adsorption of benzene and naphthalene on an infinite sheet of graphite, as well as the binding between two graphite sheets. A comparison with recent thermal-desorption data [Phys. Rev. B 69, 155406 (2004)] shows great promise for the vdW-DF method.     

分子动力学和丙氨酸变异研究MDM2与抑制剂P4的结合模式

抑制p53-MDM2相互作用已经成为癌症治疗的新途径. 采用分子动力学模拟和MM-PBSA(molecular mechanics-Possion-Boltzmann surface area)方法研究了肽类抑制剂P4与MDM2的结合模式. 研究表明P4与MDMD2疏水性裂缝的范德华作用是抑制剂结合的主导力量。采用丙氨酸变异计算研究了P4与MDM2的作用热区. 结果表明残基Lys51, Leu54, Leu57, Ile61, Met62, Tyr67, Gln72, His73, Val93, His96和Ile99的丙氨酸变异导致了范德华作用的降低, 而对极性相互作用几乎没有产生影响, 同时也证明这些残基处于P4与MDM2作用表面的热区, 对抑制剂的结合有重要贡献, 这能为抗癌药物的设计提供理论上的指导. 关键词：分子动力学; 丙氨酸变异; MM-PBSA; p53-MDM2相互作用     

分子动力学和丙氨酸变异研究MDM2与抑制剂P4的结合模式

抑制p53-MDM2相互作用已经成为癌症治疗的新途径.采用分子动力学模拟和MM-PBSA(molecular mechanics-Possion-Boltzmann surface area)方法研究了肽类抑制剂P4与MDM2的结合模式.研究表明P4与MDMD2疏水性裂缝的范德华作用是抑制剂结合的主导力量。采用丙氨酸变异计算研究了P4与MDM2的作用热区.结果表明残基Lys51,Leu54,Leu57,Ile61,Met62,Tyr67,Gln72,His73,Val93,His96和Ile99的丙氨酸变异导致了范德华作用的降低,而对极性相互作用几乎没有产生影响,同时也证明这些残基处于P4与MDM2作用表面的热区,对抑制剂的结合有重要贡献,这能为抗癌药物的设计提供理论上的指导.     

A DFT study of formaldehyde adsorption on functionalized graphene nanoribbons

Density functional theory (DFT) based ab initio calculations were done to monitor the formaldehyde (CHOH) adsorptive behavior on pristine and Ni-decorated graphene sheet. Structural optimization indicates that the formaldehyde molecule is physisorbed on the pristine sheet via partly weak van der Waals attraction having the adsorption energy of about −15.7 kcal/mol. Metal decorated sheet is able to interact with the CHOH molecule, so that single Ni atoms prefer to bind strongly at the bridge site of graphene and each metal atom bound on sheet may adsorb up to four CHOH. The findings also show that the Ni decoration on graphene surface results in some changes in electronic properties of the sheet and its E_g is remained unchanged after adsorption of CHOH molecules. It is noteworthy to say that no bond cleavage was observed for the adsorption of CHOH on Ni-decorated graphene.     

描述甲烷在Pt(110)-(21)表面的化学吸附解离的密度泛函评估

本文探讨了几种梯度近似(GGA)密度泛函及元梯度近似(meta-GGA)密度泛函在描述甲烷在重构的Pt(110)-(2×1)上的解离化学吸附作用的适用性. 金属的体相和表面结构、甲烷的吸附能量和解离能垒等被用来评估泛函的可靠性. 另外,在从头算分子动力学计算中,采用范德瓦尔斯矫正的GGA函数(optPBE-vdW)和范德瓦尔斯矫正的meta-GGA函数(MS-PBEl-rVV10）计算粘附概率. 计算结果表明,使用这两种泛函能更好地与现有的实验结果吻合,从而为发展甲烷在Pt(110)-(2×1)表面解离的可靠机器学习势能面打下重要基础.     

Effect of long-range forces on surface freezing

We examine the effect of long-range van der Waals interactions on surface freezing (SF) in linear hydrocarbon chain molecules, and the wetting criteria of the bulk liquid by the crystalline surface phase. We find that although the effect of van der Waals interactions is small for SF of normal alkanes, it is important for SF of dry and hydrated alcohols. We also find that the long-range interactions should not be ignored in the interpretation of wetting phenomena in recent experimental results. The results are in good agreement with recent experiments.     

Interaction of C60 with carbon nanotubes and graphite

The interaction of C60 with single-wall carbon nanotubes (SWNTs) and graphite is studied experimentally by thermal desorption spectroscopy and theoretically by molecular-mechanics and molecular-dynamics calculations. The van der Waals parameters and force field for C60-graphene and C60-SWNT interactions are derived from the low-coverage C60 binding energy to the graphite surface. We use these to compare the efficiency of different mechanisms by which C60 can be encapsulated into SWNTs.     

A self-consistent approach for modelling the interfacial properties and phase diagrams of Yukawa,Lennard-Jones and square-well fluids

A self-consistent density-functional approach is presented for describing the phase behaviour and interfacial tensions of van der Waals fluids represented by the hard-core Yukawa (HCY), Lennard-Jones (LJ) and square-well (SW) potentials. The excess Helmholtz energy functional is formulated in terms of a modified fundamental measure theory (MFMT) for the short-ranged repulsion and a density-gradient expansion for the van der Waals attractions. Analytical expressions for the direct correlation functions of uniform fluids are utilized to take into account the effect of van der Waals’ attraction on intermolecular correlations. For bulk phases, the density functional theory is reduced to an equation of state (EOS) that provides accurate saturation pressures and vapour–liquid phase diagrams. Near the critical region, the long-range fluctuations can be corrected by using the renormalization group (RG) theory. With the same set of molecular parameters, the theory also yields satisfactory surface tensions and interfacial density profiles at all relevant temperatures.     

The boundary element approach to Van der Waals interactions

We develop a boundary element method to calculate Van der Waals interactions for systems composed of domains of spatially constant dielectric response of a general boundary shape. We achieve this by rewriting the interaction energy expression presented in Phys. Rev. B, 62 (2000) 6997 exclusively in terms of surface integrals of surface operators. We validate this approach in the Lifshitz case and give numerical results for the interaction of two spheres as well as the van der Waals self-interaction of a uniaxial ellipsoid. Our method is simple to implement and is particularly suitable for a full, non-perturbative numerical evaluation of non-retarded van der Waals interactions between objects of a completely general shape.     

Adsorption of model charged proteins on charged surfaces with grafted polymers

The adsorption of model charged proteins on charged surfaces with and without grafted polymers is studied using a molecular approach. The ability of the polymer layer to reduce the amount of proteins adsorbed on top of the surface (primary adsorption) and at the same time to increase the adsorption of the proteins on top of the polymer layer (secondary adsorption) is presented. It is found that charging the free ends of the chains can result in an efficient way to enhance adsorption at the tip of the brush. Increasing the surface coverage of the polymers with charged free ends enhances the amount of proteins adsorbed at the tip of the polymer layer, while at the same time strongly reduces the number of proteins adsorbed directly onto the surface. The interplay between the attractive van der Waals protein-surface interactions, the steric polymer-protein interactions and the effect of the electrostatic interactions in determining the final adsorption is discussed. The manipulation of solution conditions to tune the amount of secondary adsorption is presented.     

Study on the adsorption behavior of γ-GPS on low carbon steel surfaces using RA-IR, EIS and AFM

The adsorption behavior of γ-GPS on low carbon steel surfaces was systematically investigated by reflection absorption infrared spectroscopy (RA-IR), electrochemical impedance spectroscopy (EIS) and atomic force microscopic (AFM), focusing on the changes in γ-GPS chains alignment during the adsorption process and the influence of assembly time on the chemical structures, three-dimension morphology and corrosion resisting property of γ-GPS films. The results indicated that the adsorption of γ-GPS exhibited an oscillatory phenomenon, which experienced rapid adsorption firstly, then reached maximum adsorption capacity, subsequently suffered extensive desorption, finally went through irreversible slow adsorption. The growth behavior and protective performance of γ-GPS films was closely related to the adsorption capacity and the alignment of silanol monomers. As more silanol monomers were adsorbed, the stronger the intermolecular van der Waals interactions between the γ-GPS chains would be, resulting in highly ordered γ-GPS films with excellent performance. The proposed adsorption models were used to simulate the experimental phenomena and determine the adsorption mechanisms taking place on the low carbon steel surfaces.     

Influence of complexation and solid environment on the vibrational coherence of DCl

The vibrational dynamics of DCl molecules embedded in different cryogenic matrices is studied by time resolved infrared Degenerate Four Wave Mixing experiments using the infrared free electron laser CLIO. The coherence behaviour of the D-Cl stretch in pure argon as well as in mixed argon/nitrogen van der Waals solids is investigated. Different interactions between the excited molecules and their environment are probed: the van der Waals interaction between the trapped molecules and the solid lattice and the interaction binding complexes trapped in the matrix (either the vdW interaction between DCl and nitrogen or weak H bonds in (DCl)_n clusters). The dependence of the dephasing time on the solid and on specific interactions is clearly observed.     

Adsorption behavior of iron phthalocyanine on a Ag（110） surface

An investigation on the growth behavior of FePc on a Ag(110) surface is carried out by using scanning tunneling microscopy(STM).At an FePc coverage of 3.5 ML,an ordered superstructure(densely packed) with a lateral shift is observed.The densely packed superstructure can be attributed to the substrate commensuration and the intermolecular van der Waals attractive interaction.The in-plane lateral shift in the superphase is specifically along the direction of [10] azimuth.The results provide a new perspective to understanding the intermolecular and the molecule-substrate interactions.